BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences.

The design choices underlying machine-learning (ML) models present important barriers to entry for many biologists who aim to incorporate ML in their research. Automated machine-learning (AutoML) algorithms can address many challenges that come with applying ML to the life sciences. However, these algorithms are rarely used in systems and synthetic biology studies because they typically do not explicitly handle biological sequences (e.g., nucleotide, amino acid, or glycan sequences) and cannot be easily compared with other AutoML algorithms. Here, we present BioAutoMATED, an AutoML platform for biological sequence analysis that integrates multiple AutoML methods into a unified framework. Users are automatically provided with relevant techniques for analyzing, interpreting, and designing biological sequences. BioAutoMATED predicts gene regulation, peptide-drug interactions, and glycan annotation, and designs optimized synthetic biology components, revealing salient sequence characteristics. By automating sequence modeling, BioAutoMATED allows life scientists to incorporate ML more readily into their work.

Spontaneous, simultaneous bilateral osteonecrosis of the femoral heads in a patient with sideroblastic anaemia with B-cell immunodeficiency, periodic fever and developmental delay syndrome.

Sideroblastic anaemia with B-cell immunodeficiency, periodic fever and developmental delay is a recently described, rare syndrome characterised by numerous manifestations underpinned by mutations in transfer RNA nucleotidyltransferase. The pathogenesis arises from mitochondrial dysfunction, with impaired intracellular stress response, deficient metabolism and cellular and systemic inflammation. This yields multiorgan dysfunction and early death in many patients with survivors suffering significant disability and morbidity. New cases, often youths, are still being described, expanding the horizon of recognisable phenotypes. We present a mature patient with spontaneous bilateral hip osteonecrosis that likely arises from the impaired RNA quality control and inflammation caused by this syndrome.

Sustainable Plant-Based Biopolymer Membranes for PEM Fuel Cells.

Carboxycellulose nanofibers (CNFs) promise to be a sustainable and inexpensive alternative material for polymer electrolyte membranes compared to the expensive commercial Nafion membrane. However, its practical applications have been limited by its relatively low performance and reduced mechanical properties under typical operating conditions. In this study, carboxycellulose nanofibers were derived from wood pulp by TEMPO oxidation of the hydroxyl group present on the C6 position of the cellulose chain. Then, citric acid cross-linked CNF membranes were prepared by a solvent casting method to enhance performance. Results from FT-IR spectroscopy, 13C NMR spectroscopy, and XRD reveal a chemical cross-link between the citric acid and CNF, and the optimal fuel cell performance was obtained by cross-linking 70 mL of 0.20 wt % CNF suspension with 300 µL of 1.0 M citric acid solution. The membrane electrode assemblies (MEAs), operated in an oxygen atmosphere, exhibited the maximum power density of 27.7 mW cm-2 and the maximum current density of 111.8 mA cm-2 at 80 °C and 100% relative humidity (RH) for the citric acid cross-linked CNF membrane with 0.1 mg cm-2 Pt loading on the anode and cathode, which is approximately 30 times and 22 times better, respectively, than the uncross-linked CNF film. A minimum activation energy of 0.27 eV is achieved with the best-performing citric acid cross-linked CNF membrane, and a proton conductivity of 9.4 mS cm-1 is obtained at 80 °C. The surface morphology of carboxycellulose nanofibers and corresponding membranes were characterized by FIB/SEM, SEM/EDX, TEM, and AFM techniques. The effect of citric acid on the mechanical properties of the membrane was assessed by tensile strength DMA.

Synergistic FRET assays for drug discovery targeting RyR2 channels.

A key therapeutic target for heart failure and arrhythmia is the deleterious leak through sarcoplasmic reticulum (SR) ryanodine receptor 2 (RyR2) calcium release channels. We have previously developed methods to detect the pathologically leaky state of RyR2 in adult cardiomyocytes by monitoring RyR2 binding to either calmodulin (CaM) or a biosensor peptide (DPc10). Here, we test whether these complementary binding measurements are effective as high-throughput screening (HTS) assays to discover small molecules that target leaky RyR2. Using FRET, we developed and validated HTS procedures under conditions that mimic a pathological state, to screen the library of 1280 pharmaceutically active compounds (LOPAC) for modulators of RyR2 in cardiac SR membrane preparations. Complementary FRET assays with acceptor-labeled CaM and DPc10 were used for Hit prioritization based on the opposing binding properties of CaM vs. DPc10. This approach narrowed the Hit list to one compound, Ro 90-7501, which altered FRET to suggest increased RyR2-CaM binding and decreased DPc10 binding. Follow-up studies revealed that Ro 90-7501 does not detrimentally affect myocyte Ca2+ transients. Moreover, Ro 90-7501 partially inhibits overall Ca2+ leak, as assessed by Ca2+ sparks in permeabilized rat cardiomyocytes. Together, these results demonstrate (1) the effectiveness of our HTS approach where two complementary assays synergize for Hit ranking and (2) a drug discovery process that combines high-throughput, high-precision in vitro structural assays with in situ myocyte assays of the pathologic RyR2 leak. These provide a drug discovery platform compatible with large-scale HTS campaigns, to identify agents that inhibit RyR2 for therapeutic development.

Medical student wellness in Canada: time for a national curriculum framework.

There is substantial evidence showing that medical student wellness is a worsening problem in Canada. It is apparent that medical students' wellness deteriorates throughout their training. Medical schools and their governing bodies are responding by integrating wellness into competency frameworks and accreditation standards through a combination of system- and individual-level approaches. System-level strategies that consider how policies, medical culture, and the "hidden curriculum" impact student wellness, are essential for reducing burnout prevalence and achieving optimal wellness outcomes. Individual-level initiatives such as wellness programming are widespread and more commonly used. These are often didactic, placing the onus on the student without addressing the learning environment. Despite significant progress, there is little programming consistency across schools or training levels. There is no wellness curriculum framework for Canadian undergraduate medical education that aligns with residency competencies. Creating such a framework would help align individual- and system-level initiatives and smooth the transition from medical school to residency. The framework would organize goals within relevant wellness domains, allow for local adaptability, consider basic learner needs, and be learner-informed. Physicians whose wellness has been supported throughout their training will positively contribute to the quality of patient care, work environments, and in sustaining a healthy Canadian population.

Nous disposons d'un grand nombre de données concrètes démontrant que le bien-être des étudiants en médecine au Canada se détériore tout au long de leur cheminement universitaire et que le problème s'aggrave. Alliant les approches systémique et individuelle, les facultés de médecine et leurs directions réagissent en intégrant le bien-être dans les cadres de compétences et les normes d'agrément. Les stratégies systémiques, qui tiennent compte de l'impact des politiques, de la culture médicale et du «curriculum caché¼ sur le bien-être des étudiants, sont indispensables pour prévenir l'épuisement professionnel et pour obtenir des résultats optimaux en matière de bien-être. Les initiatives au niveau individuel, comme les programmes axés sur le bien-être, sont de plus en plus répandues. Ces programmes sont souvent didactiques et ils sollicitent l'étudiant sans tenir compte de l'environnement d'apprentissage. Bien que ces initiatives aient marqué des progrès importants, il y a peu d'uniformité entre les programmes des diverses facultés et entre les niveaux de formation. Il n'y a pas de cadre pédagogique pour les programmes d'études de premier cycle axés sur le bien-être au Canada s'alignant aux compétences visées dans les programmes de résidence. La création d'un tel cadre permettrait d'harmoniser les initiatives de niveau individuel et celles de niveau systémique et de faciliter la transition de la faculté de médecine vers la résidence. Il comporterait des objectifs organisés selon les domaines de bien-être pertinents, une souplesse permettant son adaptation aux divers milieux, il tiendrait compte des besoins fondamentaux des apprenants et il serait fondé sur une consultation de ces derniers. Les médecins dont le bien-être a été soutenu tout au long de leur formation contribueront de façon positive à la qualité des soins aux patients, à leur environnement de travail et au maintien d'une population canadienne en bonne santé.

Twelve tips for designing assignments that foster independence in learning.

Independent learning refers to opportunities in which responsibility for learning shifts to learners. Providing health professions learners with independent learning opportunities can be challenging because of the often highly structured curricula of health professions education. Structured independent learning assignments that give learners the opportunity to begin developing the skills and strategies to take on self-directed opportunities in the future may lend themselves to these contexts. However, in health professions education contexts, few guidelines exist for designing effective assignments that foster independence in learning. These twelve tips provide recommendations for how to improve structured independent learning assignments for health professions learners and help them develop the skills and experience required for more self-directed opportunities and for lifelong learning.

Review of icatibant use in the Winnipeg Regional Health Authority.

BACKGROUND: This is a retrospective review of the Winnipeg Regional Health Authority's (WRHA) angioedema patients who were dispensed icatibant in hospital. Icatibant is a bradykinin B2 receptor antagonist indicated for Hereditary Angioedema (HAE) types I and II and is used off-label for HAE with normal C1INH (HAE-nC1INH) and ACE-inhibitor induced angioedema (ACEIIAE). The WRHA's use of icatibant is regulated by the Allergist on call. We characterized icatibant's use and the timeline from patient presentation, compared the real-world experience with the FAST-3 trial and hypothesized the factors which may affect response to icatibant. METHODS: Background data were collected on patients. Angioedema attack-related data included administered medications, performed investigations and the timeline to endpoints such as onset of symptom relief. Data was analyzed in R with the package "survival." Time-to-event data was analyzed using the Peto-Peto Prentice method or Mann-Whitney U-test. Data was also compared with published clinical trial data using the Sign Test. Fisher's Exact Test was used to produce descriptive statistics. RESULTS: Overall, 21 patients accounted for 23 angioedema attacks treated with icatibant. Approximately half the patients had a diagnosis of HAE-nC1IHN and half of ACEIIAE. Of those presenting with angioedema, 65% were first treated with conventional medication. Patients without a prior angioedema diagnosis were evaluated only 40-50% of the time for C4 levels or C1INH function or level. The median time from patients' arrival to the emergency department until the Allergy consultant's response was 1.77 h. Patients with HAE-nC1IHN had median times to onset of symptom relief and final clinical outcome (1.13 h, p = 0.34; 3.50 h, p = 0.11) similar to those reported in FAST-3 for HAE I/II. Patients with ACEIIAE had longer median times to onset of symptom relief (4.86 h, p = 0.01) than predicted. CONCLUSIONS: HAE-nC1INH may be an appropriate indication for treatment with icatibant. Conversely, the results of this study do not support the use of icatibant for the treatment of ACEIIAE, concordant with a growing body of literature. Patients should be stratified into groups of more- or less-likely icatibant-responders through history and laboratory investigations in order to prevent potential delays.